SYNOPSIS

distmat -sequence seqset -nucmethod list -protmethod list -ambiguous boolean -gapweight float -position integer -calculatea boolean -parametera float -outfile outfile

distmat -help

DESCRIPTION

distmat

OPTIONS

Input section

-sequence seqset

File containing a sequence alignment.

Required section

-nucmethod list

Multiple substitution correction methods for nucleotides.

-protmethod list

Multiple substitution correction methods for proteins.

Additional section

-ambiguous boolean

Option to use the ambiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins. Default value: N

-gapweight float

Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods. Default value: 0.

-position integer

Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases. Default value: 123

-calculatea boolean

This will force the calculation of parameter 'a' in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option). Default value: N

-parametera float

User defined parameter 'a' to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 (Jin et al.) and this is the default. Default value: 1.0

Output section

-outfile outfile

AUTHOR

Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.

COPYRIGHT

This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.